galaxyproject / galaxyproject/idc

Add mocked DB (226) for gtdb-tk to CVMFS

Open
#85 7 comments 0 reactions 0 assignees View on GitHub
Dominant language
Shell
Stars
10
Forks
8
PR merge metrics
No merged PRs in 30d

Description

This IWC wf fails since gtdb-tk DB is too big so memory fails in the github CI: https://github.com/galaxyproject/iwc/pull/1168
Can we upload the mock DB for 226 gtdb in CVMFS: https://data.gtdb.ecogenomic.org/releases/latest/auxillary_files/gtdbtk_package/mockup_db/mockup.tar.gz
It can be installed from the latest gtdb DM: https://github.com/galaxyproject/tools-iuc/blob/main/data_managers/data_manager_gtdbtk_database_installer/data_manager/gtdbtk_database_installer.xml

Contributor guide

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Research direction

Start by reviewing the failing IWC workflow in PR 1168 and the linked gtdbtk database manager installer XML. Inspect how the gtdb-tk 226 mockup.tar.gz source is installed and how reference data is published to CVMFS. Done means the mock database is available through CVMFS and the workflow no longer fails from the full database exceeding GitHub CI memory.

Written by the indexing model from the issue text.

Assessment

Tech stack
github, shell
Domain
ci-cd, databases, infrastructure
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
48/100

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